<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I guess by low-pass filtering you mean that in Fourier space the radial falloff scale factor is exactly 1.0 out to some frequency and then drops off gradually, where as a Gaussian convolution starts dropping from 1.0 gradually right from 0 frequency. Using different kernels (radial scale factor functions) would be easy — they just need to be defined by parameters that can be passed to the command. For low pass you probably need a minimum frequency and a maximum frequency giving the range of the rolloff.<div class=""><br class=""></div><div class="">We didn’t provide many map filtering options in Chimera 1, mostly you would use other software like EMAN2 to do that. But I can extend the capabilities in ChimeraX if there is interest.<br class=""><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 10, 2017, at 4:29 AM, Aaron Lewis <<a href="mailto:alewis@mrc-lmb.cam.ac.uk" class="">alewis@mrc-lmb.cam.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">I'd add that there is an important difference between Gaussian filtering and band-pass filtering: Gaussian filtering blurs (sharpens) everything by a specified amount, whereas low-pass (high-pass) filtering imposes a minimum amount of blurriness (sharpness). This often makes band-pass filtering the right choice for images with heterogenous resolution, because you often want to blur the noisiest, sharpest parts without blurring the smoothest, blurriest parts. Cryo-EM maps often fall in this category, and thus represent a common use case.</div><br class=""><div class="gmail_quote"><div dir="ltr" class="">On Wed, May 10, 2017 at 2:54 AM Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">This is just like ChimeraX Gaussian filtering which does a convolution with a Gaussian in Fourier space. That is relatively fast — a few seconds for a 256**3 map. You can already do sharpening with the “invert” option to the gaussian filtering command (“vol gaussian #1 1.5 invert true”). Gaussian filtering is one form of low pass filtering — others could be added. I think it would be nice to allow a very fast (10 updates per second) test filtering on a small region using a mouse drag to figure out the desired parameters. But I never spent to the time to figure out a user interface (what small region, how do you undo, how do you then apply to full map, …).<br class="">
<br class="">
Tom<br class="">
<br class="">
<br class="">
> On May 6, 2017, at 10:27 AM, Oliver Clarke <<a href="mailto:olibclarke@gmail.com" target="_blank" class="">olibclarke@gmail.com</a>> wrote:<br class="">
><br class="">
> Hi,<br class="">
><br class="">
> Has any consideration been given to adding the capacity for fourier-space map sharpening/low pass filtering to ChimeraX? I’m not sure whether or not it is feasible speed wise, but if it is it would be a very useful addition for EM, allowing one to easily try different sharpening B-factors/low pass cutoffs and save the resulting map(s).<br class="">
><br class="">
> Cheers<br class="">
> Oli<br class="">
> _______________________________________________<br class="">
> ChimeraX-users mailing list<br class="">
> <a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">
> Manage subscription:<br class="">
> <a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">
><br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">
Manage subscription:<br class="">
<a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">
</blockquote></div>
</div></blockquote></div><br class=""></div></div></body></html>